• Asian-Australasian Journal of Animal Sciences
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• v.31 no.8
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• pp.1373-1380
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• 2018

Objective: This study was designed to investigate the effects of temperature and storage time on the evolution of bacterial communities in swine manure. Methods: Manure was stored at $-20^{\circ}C$, $4^{\circ}C$, $20^{\circ}C$, or $37^{\circ}C$ and sampled at 7-day intervals over 28 days of storage, for a total of 5 time points. To assess the bacterial species present, 16S ribosomal RNA gene sequences were analyzed using pyrosequencing. Results: After normalization, 113,934 sequence reads were obtained, with an average length of $466.6{\pm}4.4bp$. The diversity indices of the communities reduced as temperature and storage time increased, and the slopes of rarefaction curves decreased from the second week in samples stored at $-20^{\circ}C$ and $4^{\circ}C$. These results indicate that the richness of the bacterial community in the manure reduced as temperature and storage time increased. Firmicutes were the dominant phylum in all samples examined, ranging from 89.3% to 98.8% of total reads, followed by Actinobacteria, which accounted for 0.6% to 7.9%. A change in community composition was observed in samples stored at $37^{\circ}C$ during the first 7 days, indicating that temperature plays an important role in determining the microbiota of swine manure. Clostridium, Turicibacter, Streptococcus, and Lactobacillus within Firmicutes, and Corynebacterium within Actinobacteria were the most dominant genera in fresh manure and all stored samples. Conclusion: Based on our findings, we propose Clostridium as an indicator genus of swine manure decomposition in an anaerobic environment. The proportions of dominant genera changed in samples stored at $20^{\circ}C$ and $37^{\circ}C$ during the fourth week. Based on these results, it was concluded that the microbial communities of swine manure change rapidly as storage time and temperature increase.

• Journal of Microbiology and Biotechnology
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• v.31 no.12
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• pp.1701-1708
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• 2021

Food safety is the most important global health issue due to foodborne pathogens after consumption of contaminated food. Foodborne bacteria such as Escherichia coli, Salmonella enterica, Staphylococcus aureus, Campylobacter spp., Bacillus cereus, Vibrio spp., Yersinia enterocolitica and Clostridium perfringens are leading causes of the majority of foodborne illnesses and deaths. These foodborne pathogens often come from the livestock feces, thus, we analyzed fecal microbial communities of three different livestock species to investigate the prevalence of foodborne pathogens in livestock feces using metagenomics analysis. Our data showed that alpha diversities of microbial communities were different according to livestock species. The microbial diversity of cattle feces was higher than that of chicken or pig feces. Moreover, microbial communities were significantly different among these three livestock species (cattle, chicken, and pig). At the genus level, Staphylococcus and Clostridium were found in all livestock feces, with chicken feces having higher relative abundances of Staphylococcus and Clostridium than cattle and pig feces. Genera Bacillus, Campylobacter, and Vibrio were detected in cattle feces. Chicken samples contained Bacillus, Listeria, and Salmonella with low relative abundance. Other genera such as Corynebacterium, Streptococcus, Neisseria, Helicobacter, Enterobacter, Klebsiella, and Pseudomonas known to be opportunistic pathogens were also detected in cattle, chicken, and pig feces. Results of this study might be useful for controlling the spread of foodborne pathogens in farm environments known to provide natural sources of these microorganisms.